RetrogeneDB ID:

retro_hsap_2785

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:46352084..46353411(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236736
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UQCRC2
Ensembl ID:ENSG00000140740
Aliases:UQCRC2, MC3DN5, QCR2, UQCR2
Description:ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]


Retrocopy-Parental alignment summary:






>retro_hsap_2785
TTTTTGAGACTTTATTCCCTCAAAGTTGCCCCCAAAGTTAAAGCCACAGCTACCCCCATAGGAGTGGCTCCACATCATCA
GGACCTTGAGATCATCAAATTTCCAAATGGTTTTATGATTTCTCCTTTGGAAAACTATGCCCTGCATCAAGAATTGGTTT
GTTCATTAAAGCAGGCAGTAGCTATGAGGACTCCAACAATTTAGTAACTTCTCATTTGCTGTGTCTTGCATCCAGTTTGA
CTACGAAAGGAGCTTCATTTTTCAAGATAGCCCATGACATTGAAGCAGCTGGTGGTAAATTAAGTGTAATTGCAACAAGA
GAAAACATAGCTTACATCATGGAATGTCTGCAGAGTGATATTGATATTCTAATGGAGTTCCTGCTCAGTGTCGCCACAGC
ACCAGGATTTGGTCATTGGGAAGTAGATGCCTTCAGTCTCAGCTAAGGATAGACAGATCTGTGAATTTTCAGAATCCACA
GGCACATGTCATTGAAAATTTGCATACTGAAGCTTATTGGGATGCCTTGGCTAATTCCTTGTATTGTCCTGGCTATAGGA
TTGGAAAAGTGACATGGGAAGAGTTACATTACTATGTTTAGAACCACTTCACAAGTGCAAGAATGGCTTGGTTGGACTTG
GTGTGAGTCACCCTGTTCTAAAGCAAGTTGCTGAATAGTTTCTCAACAGGAGGGGTGGGTTTCTTTTGTCTGGTACAAAA
GCCAAATACTCTGGAGGTGAAATTCAGGAACAAAATGGAGACAGTCTTGTCCATGCTTGCTCTTGTAGCAGAAAGTGCTG
CCACAAGAAGGGCACAGCAAATGCATTTAGTGTTTTTCAGCATATCAAGAGGGACACCATATGTCAAGGGGCACAGTGAT
GCCACCAGCTATCTATAGCAGGCTATTGCCAAGGCAATTCACCAGCCACTTGCTATTTCTGTTTTTAATGCTAGTTACTC
CAATTTTGGACTCTTCAGGATGTACATTGTCTTCCAGGCTGCAGCTGCTGGAGATGTTATCAAGGCTACCTATAACCAAG
TGGAAATAATTGCTCAAGAAAAGCTTTTCAATGTCCAGGCTGCCAAGAACAAACTGAAAGCTGGATACCAAATATAAGTG
AAGTCTTCCGAGGGTTTCATAGAAGAAGTCAGGCCCCAGGCTGTAGTTACTGGTTCTTACAAGCCAATATCACCAGTCCT
TCAGTAGATTAGTTGGTTGGCTAGTGCTGTCATCATCAATTCTGCAAAGAAGTTTGCTTCTGGCTAGAAACAAACTTCTA
CTTGTTAATGGCAACAATTGGAACATACACCTTTGGTTGATGAGTTG

ORF - retro_hsap_2785 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.22 %
Parental protein coverage: 98.01 %
Number of stop codons detected: 7
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalFSRFYSLKVAPKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYS-PVSRIGLFIKAGSRYEDFSNLG
F.R.YSLKVAPKVKATA.P.G..P..QDLE..K.PNG..I..LENY..P.SRIGLFIKAGS.YED..NL.
RetrocopyFLRLYSLKVAPKVKATATPIGVAPHHQDLEIIKFPNGFMISPLENYA<PASRIGLFIKAGSSYEDSNNLV
ParentalTTHLLRLTSSLTTKGASSFKITRGIEAVGGKLSVTATRENMAYTVECLRGDVDILMEFLLNVTTAPEFRR
T.HLL.L.SSLTTKGAS.FKI...IEA.GGKLSV.ATREN.AY..ECL..D.DILMEFLL.V.TAP.F..
RetrocopyTSHLLCLASSLTTKGASFFKIAHDIEAAGGKLSVIATRENIAYIMECLQSDIDILMEFLLSVATAPGFGH
ParentalWEVAD-LQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYFVQNHFTSAR
WEV...LQ.QL.ID..V.FQNPQ.HVIENLH..AY..ALAN.LYCP.YRIGKVT.EELHY.V.NHFTSAR
RetrocopyWEVDA<LQSQLRIDRSVNFQNPQAHVIENLHTEAYWDALANSLYCPGYRIGKVTWEELHYYV*NHFTSAR
ParentalMA-LIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKANYRGGEIREQNGDSLVHA-AFVAESAVAGSAEANA
MA.L.GLGVSHPVLKQVAE.FLN.RGG..LSG.KA.Y.GGEI.EQNGDSLVHA.A.VAESA....A....
RetrocopyMA<LVGLGVSHPVLKQVAE*FLNRRGGFLLSGTKAKYSGGEIQEQNGDSLVHA>ALVAESAATRRAQ-QM
ParentalFSVLQHVLGAGPHVKRGSNTTSHLHQAVAKATQQPFDVSAFNASYSDSGLFGIYTISQATAAGDVIKAAY
..V........P.VK..S..TS.L.QA.AKA..QP...S.FNASYS..GLF..Y...QA.AAGDVIKA.Y
RetrocopyHLVFFSISRGTPYVKGHSDATSYL*QAIAKAIHQPLAISVFNASYSNFGLFRMYIVFQAAAAGDVIKATY
ParentalNQVKTIAQGNLSNTDVQAAKNKLKAGYLMSVESSECFLEEVGSQALVAGSYMPPSTVLQQIDSVANADII
NQV..IAQ..L.N..VQAAKNKLKAGY...V.SSE.F.EEV..QA.V.GSY.P.S.VLQ.I...A.A.II
RetrocopyNQVEIIAQEKLFN--VQAAKNKLKAGYQI*VKSSEGFIEEVRPQAVVTGSYKPISPVLQ*ISWLASAVII
ParentalNAAKKFVSG--QKSMAASGNLGHTPFVDEL
N.AKKF.SG..Q.S......L.HTP.VDEL
RetrocopyNSAKKFASG*KQTSTC*WQQLEHTPLVDEL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 119 .55 RPM
bodymap2_adrenal 0 .00 RPM 102 .18 RPM
bodymap2_brain 0 .00 RPM 174 .93 RPM
bodymap2_breast 0 .00 RPM 151 .44 RPM
bodymap2_colon 0 .00 RPM 173 .23 RPM
bodymap2_heart 0 .00 RPM 473 .99 RPM
bodymap2_kidney 0 .00 RPM 209 .87 RPM
bodymap2_liver 0 .00 RPM 107 .69 RPM
bodymap2_lung 0 .00 RPM 118 .62 RPM
bodymap2_lymph_node 0 .00 RPM 93 .63 RPM
bodymap2_ovary 0 .00 RPM 121 .66 RPM
bodymap2_prostate 0 .00 RPM 217 .33 RPM
bodymap2_skeletal_muscle 0 .00 RPM 267 .93 RPM
bodymap2_testis 0 .02 RPM 102 .69 RPM
bodymap2_thyroid 0 .00 RPM 156 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 146 .97 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2785 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2785 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2785 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2785 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2785 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1886
Gorilla gorilla retro_ggor_1941
Parental genes homology:
Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000216512 retrocopies
retro_btau_1008, retro_btau_1668,
Canis familiaris ENSCAFG000000177561 retrocopy
retro_cfam_2075,
Callithrix jacchus ENSCJAG000000091161 retrocopy
retro_cjac_222,
Echinops telfairi ENSETEG000000010841 retrocopy
retro_etel_2087,
Homo sapiens ENSG00000140740 1 retrocopy
retro_hsap_2785 ,
Gorilla gorilla ENSGGOG000000153791 retrocopy
retro_ggor_1941,
Myotis lucifugus ENSMLUG000000033452 retrocopies
retro_mluc_1391, retro_mluc_770,
Macaca mulatta ENSMMUG000000182872 retrocopies
retro_mmul_1442, retro_mmul_683,
Monodelphis domestica ENSMODG000000076451 retrocopy
retro_mdom_327,
Mustela putorius furoENSMPUG000000168491 retrocopy
retro_mputfur_1042,
Nomascus leucogenys ENSNLEG000000121851 retrocopy
retro_nleu_685,
Oryctolagus cuniculus ENSOCUG000000038912 retrocopies
retro_ocun_604, retro_ocun_739,
Otolemur garnettii ENSOGAG000000054784 retrocopies
retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps ENSOPRG000000004191 retrocopy
retro_opri_455,
Pongo abelii ENSPPYG000000071741 retrocopy
retro_pabe_2232,
Pan troglodytes ENSPTRG000000078711 retrocopy
retro_ptro_1886,
Sorex araneus ENSSARG000000106701 retrocopy
retro_sara_231,
Vicugna pacos ENSVPAG000000109141 retrocopy
retro_vpac_640,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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